Experts and Doctors on gene expression profiling in Memphis, Tennessee, United States

Summary

Locale: Memphis, Tennessee, United States
Topic: gene expression profiling

Top Publications

  1. Zhou D, Zhao Y, Baker J, Gu Q, Hamre K, Yue J, et al. The effect of alcohol on the differential expression of cluster of differentiation 14 gene, associated pathways, and genetic network. PLoS ONE. 2017;12:e0178689 pubmed publisher
    ..In conclusion, we found Cd14, along with several other genes and pathways, to be involved in ethanol responses in the hippocampus, such as increased susceptibility to lipopolysaccharides and neuroinflammation. ..
  2. Lancaster C, Hu C, Franke R, Filipski K, Orwick S, Chen Z, et al. Cisplatin-induced downregulation of OCTN2 affects carnitine wasting. Clin Cancer Res. 2010;16:4789-99 pubmed publisher
    ..We postulate that this phenomenon is triggered by deactivation of peroxisome proliferator activated receptor ? and leads to deregulation of carnitine-shuttle genes. ..
  3. Caudle K, Barker K, Wiederhold N, Xu L, Homayouni R, Rogers P. Genomewide expression profile analysis of the Candida glabrata Pdr1 regulon. Eukaryot Cell. 2011;10:373-83 pubmed publisher
    ..Our results demonstrate that while CgPdr1 activates a broad repertoire of genes, specific activating mutations result in the activation of discrete subsets of this repertoire. ..
  4. Drenberg C, Gibson A, Pounds S, Shi L, Rhinehart D, Li L, et al. OCTN1 Is a High-Affinity Carrier of Nucleoside Analogues. Cancer Res. 2017;77:2102-2111 pubmed publisher
    ..i>Cancer Res; 77(8); 2102-11. ©2017 AACR. ..
  5. Kanangat S, Postlethwaite A, Cholera S, Williams L, Schaberg D. Modulation of virulence gene expression in Staphylococcus aureus by interleukin-1beta: novel implications in bacterial pathogenesis. Microbes Infect. 2007;9:408-15 pubmed
    ..Determination of the mechanisms of IL-1-induced alterations in S. aureus gene expression may lead to the identification of novel therapeutic targets against this ever-evolving opportunistic pathogen. ..
  6. Lugthart S, Cheok M, den Boer M, Yang W, Holleman A, Cheng C, et al. Identification of genes associated with chemotherapy crossresistance and treatment response in childhood acute lymphoblastic leukemia. Cancer Cell. 2005;7:375-86 pubmed
    ..The expression of these genes discriminated treatment outcome in two independent patient populations, identifying a subset of patients with a markedly inferior outcome (37% +/- 13% 5 year DFS). ..
  7. Diamond E, Durham B, Haroche J, Yao Z, Ma J, Parikh S, et al. Diverse and Targetable Kinase Alterations Drive Histiocytic Neoplasms. Cancer Discov. 2016;6:154-65 pubmed publisher
    ..Refractory patients with MAP2K1- and ARAF-mutant histiocytoses had clinical responses to MEK inhibition and sorafenib, respectively, highlighting the importance of comprehensive genomic analysis of these disorders. ..
  8. Xiao Z, Dallas M, Qiu N, NICOLELLA D, Cao L, Johnson M, et al. Conditional deletion of Pkd1 in osteocytes disrupts skeletal mechanosensing in mice. FASEB J. 2011;25:2418-32 pubmed publisher
    ..These data indicate that polycystin-1 is essential for the anabolic response to skeletal loading in osteoblasts/osteocytes. ..
  9. Zhao W, Zhao T, Chen Y, Qu Y, Gerling I, Sun Y. Modification of oxidative stress on gene expression profiling in the rat infarcted heart. Mol Cell Biochem. 2013;379:243-53 pubmed publisher
    ..These observations indicate that ROS regulate various molecular and cellular actions related to cardiac repair/remodeling through multiple gene networks. ..

More Information

Publications87

  1. Boon A, deBeauchamp J, Hollmann A, Luke J, Kotb M, Rowe S, et al. Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice. J Virol. 2009;83:10417-26 pubmed publisher
    ..One of the validated genes, the hemolytic complement gene, affected virus titer 7 days after infection. We conclude that H5N1 influenza virus-induced pathology is affected by a complex and multigenic host component...
  2. Rogers P, Thornton J, Barker K, McDaniel D, Sacks G, Swiatlo E, et al. Pneumolysin-dependent and -independent gene expression identified by cDNA microarray analysis of THP-1 human mononuclear cells stimulated by Streptococcus pneumoniae. Infect Immun. 2003;71:2087-94 pubmed
    ..These results demonstrate the striking effects of pneumolysin on the host cell upon exposure to S. pneumoniae. ..
  3. Johnson R, Wright K, Gilbertson R. Molecular profiling of pediatric brain tumors: insight into biology and treatment. Curr Oncol Rep. 2009;11:68-72 pubmed
  4. Xiao J, Thompson M, Vemula S, Ledoux M. Blepharospasm in a multiplex African-American pedigree. J Neurol Sci. 2016;362:299-303 pubmed publisher
    ..Blepharospasm can be familial and may be hereditary in African-Americans. A comprehensive array of in silico tools, and, if possible, co-segregation analysis should be used to classify SVs in dystonia-associated genes. ..
  5. Xu L, Cheng C, George E, Homayouni R. Literature aided determination of data quality and statistical significance threshold for gene expression studies. BMC Genomics. 2012;13 Suppl 8:S23 pubmed publisher
    ..These methods will assist investigators to more efficiently extract biologically meaningful insights from high throughput gene expression experiments. ..
  6. Vazquez Chona F, Khan A, Chan C, Moore A, Dash P, Hernandez M, et al. Genetic networks controlling retinal injury. Mol Vis. 2005;11:958-70 pubmed
    ..Using genetic linkage analysis of natural transcript variation, we identified regulatory loci and candidate regulators that control transcript levels of acute phase genes. ..
  7. Flotho C, Coustan Smith E, Pei D, Cheng C, Song G, Pui C, et al. A set of genes that regulate cell proliferation predicts treatment outcome in childhood acute lymphoblastic leukemia. Blood. 2007;110:1271-7 pubmed
    ..Incorporation of the expression levels of these genes into existing strategies of risk classification could improve clinical management. ..
  8. Kuo M, Duncavage E, Mathew R, den Besten W, Pei D, Naeve D, et al. Arf induces p53-dependent and -independent antiproliferative genes. Cancer Res. 2003;63:1046-53 pubmed
    ..Together, the results indicate that p19(Arf) induces a broad spectrum of proteins that likely act in concert to arrest cell proliferation. ..
  9. Rogers P, Liu T, Barker K, Hilliard G, English B, Thornton J, et al. Gene expression profiling of the response of Streptococcus pneumoniae to penicillin. J Antimicrob Chemother. 2007;59:616-26 pubmed
    ..Such genes may represent potential therapeutic targets for enhancing the activity of penicillin against this organism and provide insight into novel mechanisms of penicillin resistance. ..
  10. Mullighan C, Kennedy A, Zhou X, Radtke I, Phillips L, Shurtleff S, et al. Pediatric acute myeloid leukemia with NPM1 mutations is characterized by a gene expression profile with dysregulated HOX gene expression distinct from MLL-rearranged leukemias. Leukemia. 2007;21:2000-9 pubmed
    ..These findings suggest that mutated NPM1 leads to dysregulated HOX expression via a different mechanism than MLL rearrangement. ..
  11. Liu T, Znaidi S, Barker K, Xu L, Homayouni R, Saidane S, et al. Genome-wide expression and location analyses of the Candida albicans Tac1p regulon. Eukaryot Cell. 2007;6:2122-38 pubmed
    ..They also suggest roles for Tac1p in regulating lipid metabolism (mobilization and trafficking) and oxidative stress response in C. albicans. ..
  12. Krushkal J, Yan B, DiDonato L, Puljic M, Nevin K, Woodard T, et al. Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a relGsu mutant. Funct Integr Genomics. 2007;7:229-55 pubmed
    ..These findings suggest that Fur- and RpoS-dependent gene expression in G. sulfurreducens is affected by Rel(Gsu)-mediated signaling...
  13. Pounds S, Gao C, Johnson R, Wright K, Poppleton H, Finkelstein D, et al. A procedure to statistically evaluate agreement of differential expression for cross-species genomics. Bioinformatics. 2011;27:2098-103 pubmed publisher
    ..An R package is currently available from www.stjuderesearch.org/site/depts/biostats/agdex and will shortly be available from www.bioconductor.org. ..
  14. Thompson M, Fuller C, Hogg T, Dalton J, Finkelstein D, Lau C, et al. Genomics identifies medulloblastoma subgroups that are enriched for specific genetic alterations. J Clin Oncol. 2006;24:1924-31 pubmed
    ..This approach may assist ultimately in the selection of patients for future clinical trials of molecular targeted therapies. ..
  15. Dou W, Thompson Jaeger S, Laulederkind S, Becker J, Montgomery J, Ruiz Bustos E, et al. Defective expression of Tamm-Horsfall protein/uromodulin in COX-2-deficient mice increases their susceptibility to urinary tract infections. Am J Physiol Renal Physiol. 2005;289:F49-60 pubmed
    ..Finally, we demonstrate that the bladders of COX-2 -/- mice, in contrast to those of the wild-type mice, are highly susceptible to colonization by uropathogenic Escherichia coli. ..
  16. Gatzka M, Piekorz R, Moriggl R, Rawlings J, Ihle J. A role for STAT5A/B in protection of peripheral T-lymphocytes from postactivation apoptosis: insights from gene expression profiling. Cytokine. 2006;34:143-54 pubmed
  17. French D, Yang W, Cheng C, Raimondi S, Mullighan C, Downing J, et al. Acquired variation outweighs inherited variation in whole genome analysis of methotrexate polyglutamate accumulation in leukemia. Blood. 2009;113:4512-20 pubmed publisher
    ..We conclude that acquired genetic variation in leukemia cells has a stronger influence on MTXPG accumulation than inherited genetic variation. ..
  18. Zhao W, Hevener K, White S, Lee R, Boyett J. A statistical framework to evaluate virtual screening. BMC Bioinformatics. 2009;10:225 pubmed publisher
    ..The theoretical null distribution of SLR metric is available so that the threshold of SLR can be exactly determined without resorting to bootstrap simulations, which makes it easy to use in practical virtual screening studies. ..
  19. Geisert E, Lu L, Freeman Anderson N, Templeton J, Nassr M, Wang X, et al. Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice. Mol Vis. 2009;15:1730-63 pubmed
    ..The integration of these data into GeneNetwork provides users with a workbench to test linkages between sequence differences and eye structure and function. ..
  20. Nedelsky N, Pennuto M, Smith R, Palazzolo I, Moore J, Nie Z, et al. Native functions of the androgen receptor are essential to pathogenesis in a Drosophila model of spinobulbar muscular atrophy. Neuron. 2010;67:936-52 pubmed publisher
    ..These findings indicate that SBMA pathogenesis is mediated by misappropriation of native protein function, a mechanism that may apply broadly to polyglutamine diseases...
  21. Ouyang X, Tran Q, Goodwin S, Wible R, Sutter C, Sutter T. Yap1 activation by H2O2 or thiol-reactive chemicals elicits distinct adaptive gene responses. Free Radic Biol Med. 2011;50:1-13 pubmed publisher
    ..These findings demonstrate that the distinct mechanisms of Yap1 activation by H(2)O(2) or thiol-reactive chemicals result in selective expression of protective genes...
  22. Geng X, Lavado A, Lagutin O, Liu W, Oliver G. Expression of Six3 Opposite Strand (Six3OS) during mouse embryonic development. Gene Expr Patterns. 2007;7:252-7 pubmed
    ..Our results show that Six3OS expression overlaps extensively with that of Six3 and is not altered in Six3-null embryos. ..
  23. Zhao W, Langfelder P, Fuller T, Dong J, Li A, Hovarth S. Weighted gene coexpression network analysis: state of the art. J Biopharm Stat. 2010;20:281-300 pubmed publisher
    ..In this article, we review key concepts of WGCNA and some of its applications in gene expression analysis of oncology, brain function, and protein interaction data. ..
  24. Lavado A, Oliver G. Prox1 expression patterns in the developing and adult murine brain. Dev Dyn. 2007;236:518-24 pubmed
    ..In adulthood, Prox1 expression remains only in the hippocampus and cerebellum. These complex patterns of expression suggest that Prox1 activity is differentially required during brain development and adulthood. ..
  25. Kanangat S, Postlethwaite A, Hasty K, Kang A, Smeltzer M, Appling W, et al. Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections. Arthritis Res Ther. 2006;8:R176 pubmed
    ..aureus treatment. We propose that host-derived MMPs contribute to the progressive joint destruction observed in S. aureus-mediated septic arthritis. ..
  26. Walker A, Steward S, Howard T, Mortier N, Smeltzer M, Wang Y, et al. Epigenetic and molecular profiles of erythroid cells after hydroxyurea treatment in sickle cell anemia. Blood. 2011;118:5664-70 pubmed publisher
    ..This study was registered at ClinicalTrials.gov (NCT00305175)...
  27. Shaik J, Yeasin M. A unified framework for finding differentially expressed genes from microarray experiments. BMC Bioinformatics. 2007;8:347 pubmed
    ..Empirical analyses show that the unified framework outperformed other gene selection methods in selecting differentially expressed genes from microarray data. ..
  28. Dai B, David V, Martin A, Huang J, Li H, Jiao Y, et al. A comparative transcriptome analysis identifying FGF23 regulated genes in the kidney of a mouse CKD model. PLoS ONE. 2012;7:e44161 pubmed publisher
    ..These gene products provide a possible mechanistic links between elevated FGF23 and pathways responsible for renal failure progression and cardiovascular diseases. ..
  29. Garrison S, Jeffers J, Yang C, Nilsson J, Hall M, Rehg J, et al. Selection against PUMA gene expression in Myc-driven B-cell lymphomagenesis. Mol Cell Biol. 2008;28:5391-402 pubmed publisher
    ..These findings establish that PUMA is silenced in human malignancies, and they suggest PUMA as a target for the development of novel chemotherapeutics. ..
  30. Kasper L, Lerach S, Wang J, Wu S, Jeevan T, Brindle P. CBP/p300 double null cells reveal effect of coactivator level and diversity on CREB transactivation. EMBO J. 2010;29:3660-72 pubmed publisher
    ..This model suggests how gene expression patterns could be tuned by altering coactivator availability rather than by changing signal input or transcription factor levels. ..
  31. Wagner L, Burger R, Guichard S, Raimondi S, Santana V, Furman W, et al. Pilot study to evaluate MYCN expression as a neuroblastoma cell marker to detect minimal residual disease by RT-PCR. J Pediatr Hematol Oncol. 2006;28:635-41 pubmed
    ..The selective expression of MYCN in tumor cells, and the sensitivity of detection of MYCN by RT-PCR noted in this and other studies, supports further evaluation of MYCN as a NB marker for molecular detection of minimal residual disease. ..
  32. Roberts K, Mullighan C. How new advances in genetic analysis are influencing the understanding and treatment of childhood acute leukemia. Curr Opin Pediatr. 2011;23:34-40 pubmed publisher
    ..Future studies will be increasingly reliant on comprehensive genomic sequencing to reveal the spectrum of genetic alterations in this disease, with the ultimate aim of improving the treatment outcome for leukemia patients. ..
  33. Yang K, Neale G, Green D, He W, Chi H. The tumor suppressor Tsc1 enforces quiescence of naive T cells to promote immune homeostasis and function. Nat Immunol. 2011;12:888-97 pubmed publisher
    ..Therefore, Tsc1-dependent control of mTOR is crucial in actively maintaining the quiescence of naive T cells to facilitate adaptive immune function. ..
  34. Parsons J, Kukula M, Jackson P, Pulse M, Simecka J, Valtierra D, et al. Perturbation of Staphylococcus aureus gene expression by the enoyl-acyl carrier protein reductase inhibitor AFN-1252. Antimicrob Agents Chemother. 2013;57:2182-90 pubmed publisher
    ..These data indicate that the effects of AFN-1252 on virulence factor gene expression depend on the physiological state of the bacteria. ..
  35. Lamba J, Lamba V, Yasuda K, Lin Y, Assem M, Thompson E, et al. Expression of constitutive androstane receptor splice variants in human tissues and their functional consequences. J Pharmacol Exp Ther. 2004;311:811-21 pubmed
    ..The expression of CAR in additional human cell types increases the range of tissue specific transcriptional responses regulated by this receptor, suggesting additional biological roles for CAR and CAR-SV proteins in these tissues. ..
  36. Paugh B, Qu C, Jones C, Liu Z, Adamowicz Brice M, Zhang J, et al. Integrated molecular genetic profiling of pediatric high-grade gliomas reveals key differences with the adult disease. J Clin Oncol. 2010;28:3061-8 pubmed publisher
    ..PDGFRalpha may be a useful target for pediatric HGG, including diffuse pontine gliomas. ..
  37. Liu J, Huang Q, Higdon J, Liu W, Xie T, Yamashita T, et al. Distinct gene expression profiles and reduced JNK signaling in retinitis pigmentosa caused by RP1 mutations. Hum Mol Genet. 2005;14:2945-58 pubmed
    ..Our studies further suggest JNK-related therapeutic strategies for RP1 diseases. ..
  38. Wu G, Diaz A, Paugh B, Rankin S, Ju B, Li Y, et al. The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nat Genet. 2014;46:444-450 pubmed publisher
    ..This comprehensive analysis provides insights into the unique and shared pathways driving pediatric HGG within and outside the brainstem. ..
  39. Genthe J, Min J, Farmer D, Shelat A, Grenet J, Lin W, et al. Ventromorphins: A New Class of Small Molecule Activators of the Canonical BMP Signaling Pathway. ACS Chem Biol. 2017;12:2436-2447 pubmed publisher
  40. Paugh B, Broniscer A, Qu C, Miller C, Zhang J, Tatevossian R, et al. Genome-wide analyses identify recurrent amplifications of receptor tyrosine kinases and cell-cycle regulatory genes in diffuse intrinsic pontine glioma. J Clin Oncol. 2011;29:3999-4006 pubmed publisher
    ..We evaluated a large cohort of DIPGs to identify recurrent genomic abnormalities and gene expression signatures underlying DIPG...
  41. Wei L, Fan M, Xu L, Heinrich K, Berry M, Homayouni R, et al. Bioinformatic analysis reveals cRel as a regulator of a subset of interferon-stimulated genes. J Interferon Cytokine Res. 2008;28:541-51 pubmed publisher
    ..Thus, our studies identify cRel as an important TF for ISGs, and validate the approach of using Latent Semantic Indexing (LSI)-based methods to identify regulatory factors from microarray data. ..
  42. Jensen L, Farook M, Reiter L. Proteomic profiling in Drosophila reveals potential Dube3a regulation of the actin cytoskeleton and neuronal homeostasis. PLoS ONE. 2013;8:e61952 pubmed publisher
    ..The identification of UBE3A targets is the first step in unraveling the molecular etiology of AS and duplication 15q autism. ..
  43. Inaba H, Greaves M, Mullighan C. Acute lymphoblastic leukaemia. Lancet. 2013;381:1943-55 pubmed publisher
  44. McEvoy J, Flores Otero J, Zhang J, Nemeth K, Brennan R, Bradley C, et al. Coexpression of normally incompatible developmental pathways in retinoblastoma genesis. Cancer Cell. 2011;20:260-75 pubmed publisher
    ..Furthermore, neurotransmitter receptors, transporters, and biosynthetic enzymes are expressed in human retinoblastoma, and targeted disruption of these pathways reduces retinoblastoma growth in vivo and in vitro. ..
  45. Zaza G, Yang W, Kager L, Cheok M, Downing J, Pui C, et al. Acute lymphoblastic leukemia with TEL-AML1 fusion has lower expression of genes involved in purine metabolism and lower de novo purine synthesis. Blood. 2004;104:1435-41 pubmed
    ..These findings have established that TEL-AML1 ALL has significantly lower de novo purine synthesis and differential expression of genes involved in purine metabolism. ..
  46. Kulkarni A, Pillai R, Ezekiel A, Henner W, Handorf C. Comparison of histopathology to gene expression profiling for the diagnosis of metastatic cancer. Diagn Pathol. 2012;7:110 pubmed publisher
    ..A larger comparative effectiveness study using this study design is needed to confirm the results. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1749854104745508. ..
  47. Mullighan C, Downing J. Genome-wide profiling of genetic alterations in acute lymphoblastic leukemia: recent insights and future directions. Leukemia. 2009;23:1209-18 pubmed publisher
    ..Here, we review recent data obtained from genome-wide profiling studies in ALL, and discuss potential avenues for future investigation. ..
  48. Taylor M, Poppleton H, Fuller C, Su X, Liu Y, Jensen P, et al. Radial glia cells are candidate stem cells of ependymoma. Cancer Cell. 2005;8:323-35 pubmed
  49. Torchia E, Boyd K, Rehg J, Qu C, Baker S. EWS/FLI-1 induces rapid onset of myeloid/erythroid leukemia in mice. Mol Cell Biol. 2007;27:7918-34 pubmed
    ..The Cre-inducible EWS/FLI-1 mouse provides a novel model system to study the contribution of this oncogene to malignant disease in vivo. ..
  50. Chen J, Coustan Smith E, Suzuki T, Neale G, Mihara K, Pui C, et al. Identification of novel markers for monitoring minimal residual disease in acute lymphoblastic leukemia. Blood. 2001;97:2115-20 pubmed
    ..These results indicate that studies of gene expression with cDNA arrays can aid the discovery of leukemia markers. (Blood. 2001;97:2115-2120) ..
  51. Edick M, Cheng C, Yang W, Cheok M, Wilkinson M, Pei D, et al. Lymphoid gene expression as a predictor of risk of secondary brain tumors. Genes Chromosomes Cancer. 2005;42:107-16 pubmed
    ..These data suggest that gene expression profiling from accessible tissues may identify targets involved in therapy-related malignancies in unrelated tissues. ..
  52. French D, Wilkinson M, Yang W, de Chaisemartin L, Cook E, Das S, et al. Global gene expression as a function of germline genetic variation. Hum Mol Genet. 2005;14:1621-9 pubmed
  53. Arora N, Wenzel P, McKinney Freeman S, Ross S, Kim P, Chou S, et al. Effect of developmental stage of HSC and recipient on transplant outcomes. Dev Cell. 2014;29:621-628 pubmed publisher
    ..Adult BM-derived HSCs preferentially homed to the liver in neonatal mice yet showed balanced homing to the liver and spleen in adults. These findings emphasize the functional differences between nascent and mature definitive HSCs. ..
  54. Wang J, Kilic G, Aydin M, Burke Z, Oliver G, Sosa Pineda B. Prox1 activity controls pancreas morphogenesis and participates in the production of "secondary transition" pancreatic endocrine cells. Dev Biol. 2005;286:182-94 pubmed
    ..Prox1 thus appears to be an essential component of a genetic program destined to produce the cellular complexity of the mammalian pancreas. ..
  55. Flotho C, Coustan Smith E, Pei D, Iwamoto S, Song G, Cheng C, et al. Genes contributing to minimal residual disease in childhood acute lymphoblastic leukemia: prognostic significance of CASP8AP2. Blood. 2006;108:1050-7 pubmed
    ..Therefore, this gene is a strong candidate for inclusion in gene expression arrays specifically designed for leukemia diagnosis. ..
  56. Gruber T, Larson Gedman A, Zhang J, Koss C, Marada S, Ta H, et al. An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia. Cancer Cell. 2012;22:683-97 pubmed publisher
    ..These data suggest that expression of CBFA2T3-GLIS2 directly contributes to leukemogenesis...
  57. Yan J, Jiao Y, Jiao F, Stuart J, Donahue L, Beamer W, et al. Effects of carbonic anhydrase VIII deficiency on cerebellar gene expression profiles in the wdl mouse. Neurosci Lett. 2007;413:196-201 pubmed
    ..Several of the upregulated genes encode proteins that function in the Golgi apparatus which suggests that Car8 deficiency has important effects on synaptic vesicle formation and transport. ..
  58. Lee Y, Miller H, Jensen P, Hernan R, Connelly M, Wetmore C, et al. A molecular fingerprint for medulloblastoma. Cancer Res. 2003;63:5428-37 pubmed
    ..Coordinated deregulation of these same genes also occurred in a large subset of human medulloblastomas. These data identify a group of genes that is central to medulloblastoma tumorigenesis. ..
  59. Asano K, Duntsch C, Zhou Q, Weimar J, Bordelon D, Robertson J, et al. Correlation of N-cadherin expression in high grade gliomas with tissue invasion. J Neurooncol. 2004;70:3-15 pubmed
    ..In summary, these data collectively demonstrate that N-cadherin levels are important in the malignant behavior of gliomas, and may serve as a prognostic indicator for patients with high-grade gliomas. ..
  60. Sun Y, Boyd K, Xu W, Ma J, Jackson C, Fu A, et al. Acute myeloid leukemia-associated Mkl1 (Mrtf-a) is a key regulator of mammary gland function. Mol Cell Biol. 2006;26:5809-26 pubmed
    ..Despite the importance of Srf in multiple transcriptional pathways and widespread Mkl1 expression, the spectrum of abnormalities associated with Mkl1 absence appears surprisingly restricted. ..
  61. Mullighan C. Molecular genetics of B-precursor acute lymphoblastic leukemia. J Clin Invest. 2012;122:3407-15 pubmed publisher
    ..This article reviews these advances, discusses results from ongoing second-generation sequencing studies of ALL, and highlights challenges and opportunities for future genetic profiling approaches. ..
  62. Sadasivan S, Pond B, Pani A, Qu C, Jiao Y, Smeyne R. Methylphenidate exposure induces dopamine neuron loss and activation of microglia in the basal ganglia of mice. PLoS ONE. 2012;7:e33693 pubmed publisher
    ..Collectively, our results suggest that chronic MPH usage in mice at doses spanning the therapeutic range in humans, especially at prolonged higher doses, has long-term neurodegenerative consequences. ..
  63. Majumdar G, Rooney R, Johnson I, Raghow R. Panhistone deacetylase inhibitors inhibit proinflammatory signaling pathways to ameliorate interleukin-18-induced cardiac hypertrophy. Physiol Genomics. 2011;43:1319-33 pubmed publisher
    ..Evidently, both TSA and CBHA caused a two- to fourfold induction of phosphatase and tensin homolog expression to counteract IL-18-induced proinflammatory signaling and cardiac hypertrophy. ..
  64. Sasai K, Romer J, Kimura H, Eberhart D, Rice D, Curran T. Medulloblastomas derived from Cxcr6 mutant mice respond to treatment with a smoothened inhibitor. Cancer Res. 2007;67:3871-7 pubmed
    ..We found that transplanted tumors were dramatically inhibited in mice treated for only 4 days with HhAntag. These findings suggest that HhAntag may be effective against tumors lacking mutations in known Shh pathway genes. ..
  65. Freeman N, Templeton J, Orr W, Lu L, Williams R, Geisert E. Genetic networks in the mouse retina: growth associated protein 43 and phosphatase tensin homolog network. Mol Vis. 2011;17:1355-72 pubmed
    ..The Gap43 and Pten network highlights the covariance of gene expression and forms a molecular network associated with axonal outgrowth in the adult retina. ..
  66. Tran Q, Xu L, Phan V, Goodwin S, Rahman M, Jin V, et al. Chemical genomics of cancer chemopreventive dithiolethiones. Carcinogenesis. 2009;30:480-6 pubmed publisher
    ..Together, these findings provide new insight into the actions of clinically relevant and lead dithiolethione analogues. ..
  67. Phan V, Olusegun George E, Tran Q, Goodwin S, Bodreddigari S, Sutter T. Analyzing microarray data with transitive directed acyclic graphs. J Bioinform Comput Biol. 2009;7:135-56 pubmed
    ..The advantages and overall utility of the method in elaborating drug structure activity relationships are exemplified in a controlled study with real and simulated data. ..
  68. Davenport J, Neale G, Goorha R. Identification of genes potentially involved in LMO2-induced leukemogenesis. Leukemia. 2000;14:1986-96 pubmed
    ..Our study demonstrates that cDNA-RDA using very small amounts of total RNA is a highly efficient method to identify novel genes that may play a role in leukemogenesis. ..
  69. Sharp B, Chen H, Gong S, Wu X, Liu Z, Hiler K, et al. Gene expression in accumbens GABA neurons from inbred rats with different drug-taking behavior. Genes Brain Behav. 2011;10:778-88 pubmed publisher
    ..In Lewis rats, upregulation of Mint-1, Cask, CamkII , Ncam1, Vsnl1, Hpcal1 and Car8 indicates that these transcripts likely contribute to altered signaling and synaptic function in NAcc GABA projection neurons to VP. ..
  70. Rao S, Pavicevic Z, Du Z, Kim J, Fan M, Jiao Y, et al. Pro-inflammatory genes as biomarkers and therapeutic targets in oral squamous cell carcinoma. J Biol Chem. 2010;285:32512-21 pubmed publisher
    ..Taken together our studies indicate a strong link between inflammation and OSCC development and reveal IL-8 as a potential mediator. Treatment based on prevention of general inflammation and/or the NF-?B pathway shows promise in OSCCs...
  71. Chow L, Endersby R, Zhu X, Rankin S, Qu C, Zhang J, et al. Cooperativity within and among Pten, p53, and Rb pathways induces high-grade astrocytoma in adult brain. Cancer Cell. 2011;19:305-16 pubmed publisher
    ..Gene expression profiling revealed striking similarities to subclasses of human diffuse astrocytoma. Astrocytomas were found within and outside of proliferative niches in the adult brain. ..
  72. Ciobanu D, Lu L, Mozhui K, Wang X, Jagalur M, Morris J, et al. Detection, validation, and downstream analysis of allelic variation in gene expression. Genetics. 2010;184:119-28 pubmed publisher
    ..Using a systems genetics approach we show that two validated cis-modulated genes, Stk25 and Rasd2, are likely to control expression of downstream targets and affect disease susceptibility. ..
  73. Liu T, Lee R, Barker K, Lee R, Wei L, Homayouni R, et al. Genome-wide expression profiling of the response to azole, polyene, echinocandin, and pyrimidine antifungal agents in Candida albicans. Antimicrob Agents Chemother. 2005;49:2226-36 pubmed
    ..Genes responding similarly to two or more drugs were also identified. These data shed new light on the effects of these classes of antifungal agents on C. albicans. ..
  74. Li Q, Bohin N, Wen T, Ng V, Magee J, Chen S, et al. Oncogenic Nras has bimodal effects on stem cells that sustainably increase competitiveness. Nature. 2013;504:143-147 pubmed publisher
    ..One signal can therefore increase HSC proliferation, competitiveness and self-renewal through bimodal effects on HSC gene expression, cycling and reconstituting potential. ..
  75. Kasper L, Boussouar F, Boyd K, Xu W, Biesen M, Rehg J, et al. Two transactivation mechanisms cooperate for the bulk of HIF-1-responsive gene expression. EMBO J. 2005;24:3846-58 pubmed
    ..Our findings suggest that a novel functional interaction between the protein acetylases CBP and p300, and deacetylases, is essential for nearly all HIF-responsive transcription. ..
  76. Jiao Y, Lu L, Williams R, Smeyne R. Genetic dissection of strain dependent paraquat-induced neurodegeneration in the substantia nigra pars compacta. PLoS ONE. 2012;7:e29447 pubmed publisher
  77. Iwamoto S, Mihara K, Downing J, Pui C, Campana D. Mesenchymal cells regulate the response of acute lymphoblastic leukemia cells to asparaginase. J Clin Invest. 2007;117:1049-57 pubmed
    ..These results provide what we believe to be a new basis for understanding asparaginase resistance in ALL and indicate that MSC niches in the bone marrow can form a safe haven for leukemic cells. ..
  78. Johnson R, Wright K, Poppleton H, Mohankumar K, Finkelstein D, Pounds S, et al. Cross-species genomics matches driver mutations and cell compartments to model ependymoma. Nature. 2010;466:632-6 pubmed publisher
    ..Our data demonstrate the power of cross-species genomics to meticulously match subgroup-specific driver mutations with cellular compartments to model and interrogate cancer subgroups...